: DNA rearrangements mediated by site-specific recombinases have important biological consequences. For example, site-specific recombination is responsible for integration and excision of phage genomes in bacteria, stable propagation of bacterial chromosomes during cell division, developmental control of gene expression in prokaryotes and copy number maintenance of extrachromosomal elements in yeasts. Understanding the mechanism of site-specific recombination will help us better understand DNA rearrangements that occur in living beings, prokaryotic as well as eukaryotic. Furthermore, the knowledge can be used to manipulate the reaction in a number of useful ways: to bring about targeted genetic alterations in bacteria, yeasts, plants, flies and mammalian systems. We have used the Flp site-specific recombinase from Saccharomyces cerevisiae as a simple model system for exploring the DNA-protein interactions and the chemical steps involved in the strand breakage and joining reactions. These studies have unveiled several global mechanistic features that characterize the recombination reactions carried out by the Integrase/Tyrosine family of proteins. We will now utilize the currently available molecular genetic, biochemical and structural information to further tackle some of the unsolved questions in the Flp system.